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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 1,621 records · Page 90
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Structure and Dynamics of CO 2 at the Air–Water Interface from Classical and Neural Network Potentials

The accurate description of the structure and dynamics of CO 2 at the instantaneous air–water interface, along with the effects of surface fluctuations on the CO 2 -transport processes, is essential for the development of negative emission technologies aimed at minimizing climate change. In this study, we performed molecular dynamics simulations of CO 2 at the air–water interface using neural network potentials (NNPs) trained on ab initio data generated through density-functional-theory-based molecular dynamics simulations. We compared these results with classical force fields to assess their performance in modeling interfacial CO 2 behavior. Our findings revealed that the asymmetric interactions, coupled with thermal surface fluctuations at the air–water interface, significantly influence CO 2 transport into the aqueous phase. The simulations demonstrate that classical force fields underestimate both the free energy of CO 2 transport and the strength of its interactions at the interface compared with the neural network potentials. In conclusion, the free energy and the interfacial dynamics of CO 2 are primarily influenced by the distribution of water within the instantaneous interfacial water layer, responsible for creating an asymmetric intermolecular interaction environment within the interfacial region.

Ab initio molecular dynamics↗
DOE OSTI2013

On Eliminating Synchronous Communication in Molecular Simulations to Improve Scalability

Molecular dynamics simulation, as a complementary tool to experimentation, has become an important methodology for the understanding and design of molecular systems as it provides access to properties that are difficult, impossible or prohibitively expensive to obtain experimentally. Many of the available software packages have been parallelized to take advantage of modern massively concurrent processing resources. The challenge in achieving parallel efficiency is commonly attributed to the fact that molecular dynamics algorithms are communication intensive. This paper illustrates how an appropriately chosen data distribution and asynchronous one-sided communication approach can be used to effectively deal with the data movement within the Global Arrays/ARMCI programming model framework. A new put_notify capability is presented here, allowing the implementation of the molecular dynamics algorithm without any explicit global or local synchronization or global data reduction operations. In addition, this push-data model is shown to very effectively allow hiding data communication behind computation. Rather than data movement or explicit global reductions, the implicit synchronization of the algorithm becomes the primary challenge for scalability. Without any explicit synchronous operations, the scalability of molecular simulations is shown to depend only on the ability to evenly balance computational load.

Straatsma, TP↗
DOE OSTI2014

A multiscale mass scaling approach for explicit time integration using proper orthogonal decomposition

One of the main computational issues with explicit dynamics simulations is the significant reduction of the critical time step as the spatial resolution of the finite element mesh increases. In this work, a selective mass scaling approach is presented that can significantly reduce the computational cost in explicit dynamic simulations, while maintaining accuracy. The proposed method is based on a multiscale decomposition approach that separates the dynamics of the system into low (coarse scales) and high frequencies (fine scales). Here, the critical time step is increased by selectively applying mass scaling on the fine scale component only. In problems where the response is dominated by the coarse (low frequency) scales, significant increases in the stable time step can be realized. In this work, we use the proper orthogonal decomposition (POD) method to build the coarse scale space. The main idea behind POD is to obtain an optimal low-dimensional orthogonal basis for representing an ensemble of high-dimensional data. In our proposed method, the POD space is generated with snapshots of the solution obtained from early times of the full-scale simulation. The example problems addressed in this work show significant improvements in computational time, without heavily compromising the accuracy of the results.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2014

Interaction and dynamics of (alkylamide + electrolyte) deep eutectics: Dependence on alkyl chain-length, temperature, and anion identity

Here we investigate the solute-medium interaction and solute-centered dynamics in (RCONH{sub 2} + LiX) deep eutectics (DEs) via carrying out time-resolved fluorescence measurements and all-atom molecular dynamics simulations at various temperatures. Alkylamides (RCONH{sub 2}) considered are acetamide (CH{sub 3}CONH{sub 2}), propionamide (CH{sub 3}CH{sub 2}CONH{sub 2}), and butyramide (CH{sub 3}CH{sub 2}CH{sub 2}CONH{sub 2}); the electrolytes (LiX) are lithium perchlorate (LiClO{sub 4}), lithium bromide (LiBr), and lithium nitrate (LiNO{sub 3}). Differential scanning calorimetric measurements reveal glass transition temperatures (T{sub g}) of these DEs are ∼195 K and show a very weak dependence on alkyl chain-length and electrolyte identity. Time-resolved and steady state fluorescence measurements with these DEs have been carried out at six-to-nine different temperatures that are ∼100–150 K above their individual T{sub g}s. Four different solute probes providing a good spread of fluorescence lifetimes have been employed in steady state measurements, revealing strong excitation wavelength dependence of probe fluorescence emission peak frequencies. Extent of this dependence, which shows sensitivity to anion identity, has been found to increase with increase of amide chain-length and decrease of probe lifetime. Time-resolved measurements reveal strong fractional power dependence of average rates for solute solvation and rotation with fraction power being relatively smaller (stronger viscosity decoupling) for DEs containing longer amide and larger (weaker decoupling) for DEs containing perchlorate anion. Representative all-atom molecular dynamics simulations of (CH{sub 3}CONH{sub 2} + LiX) DEs at different temperatures reveal strongly stretched exponential relaxation of wavevector dependent acetamide self dynamic structure factor with time constants dependent both on ion identity and temperature, providing justification for explaining the fluorescence results in terms of temporal heterogeneity and amide clustering in these multi-component melts.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2014

Quantitatively Probing the Al Distribution in Zeolites

The degree of substitution of Si4+ by Al3+ in the oxygen-terminated tetrahedra (Al T-sites) of zeolites determines the concentration of ion-exchange and Brønsted acid sites. As the location of the tetrahedra and the associated subtle variations in bond angles influence the acid strength, quantitative information about Al T-sites in the framework is critical to rationalize catalytic properties and to design new catalysts. A quantitative analysis is reported that uses a combination of extended X-ray absorption fine structure (EXAFS) analysis and 27Al MAS NMR spectroscopy supported by DFT-based molecular dynamics simulations. To discriminate individual Al atoms, sets of ab initio EXAFS spectra for various T-sites are generated from DFT-based molecular dynamics simulations allowing quantitative treatment of the EXAFS single- and multiple-photoelectron scattering processes out to 3-4 atom shells surrounding the Al absorption center. It is observed that identical zeolite types show dramatically different Al-distributions. A preference of Al for T-sites that are part of one or more 4-member rings in the framework over those T-sites that are part of only 5- and 6-member rings in the HBEA150 sample has been determined from a combination of these methods. This work was supported by the U. S. Department of Energy (DOE), Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences & Biosciences.

aluminum↗
DOE OSTI2022

Mooring System Cost Estimates for Wave Energy Farms in Shared Mooring Arrays

As wave energy converters (WECs) become more advanced and cost-efficient, so too must their mooring systems. A key question in the development plans for WECs is the cost of the mooring system, particularly for large wave farms. WEC devices deployed in a WEC farm array, where each device can be connected by shared mooring lines in various array layouts, have potential to reduce mooring system costs significantly. This paper presents the modeling and designing of mooring systems for large WEC arrays and the calculation of the cost of each mooring system to determine the change in cost as the number of WECs in a farm increases. A baseline mooring system for a single floating oscillating water column (OWC) WEC was developed for this analysis. The mooring system utilizes four anchored mooring lines connected to a square assembly of wire rope mooring lines, supported by four floating buoys, and attached to the floating WEC by four polyester rope mooring lines. This assembly, referred to as a floating cell, can be tiled to form various rectangular WEC arrays. The objective of this analysis is to determine how the mooring system cost changes as more WECs are added to an array layout, each with their own interconnected floating cell. To do this, complete mooring systems need to be designed for each WEC array layout. To narrow down the design space of a WEC array mooring system, a couple assumptions were made. It was assumed that the floating cell parameters of the baseline design were to stay constant across all floating cells in the WEC array. It was also assumed that the anchored mooring lines would be of the baseline configuration, a predominantly chain mooring line with a short section of polyester rope near the fairlead, and a drag-embedment anchor. These anchored lines were assumed to extend from the outer edges of the WEC array, inline with the headings of the wire rope mooring lines of the floating cells, or diagonal if extending from a corner of the WEC array. Full mooring systems were designed for 2xN and NxN WEC array layouts and efficiently simulated in the mooring dynamics simulation tool, MoorDyn, to ensure all dynamic constraints were met. The system costs were calculated and then refined by shortening unnecessary chain line lengths and reducing the chain diameters of the downstream anchored mooring lines. It was found that, in general, mooring system costs per WEC decrease when WECs are installed in an array. Compared to the baseline mooring system for a single WEC, the 2x3 mooring system array had the lowest mooring system cost per WEC, reducing the cost per WEC by 59%. The 3x3 and 4x4 array mooring systems also saw significant reductions in cost per WEC but had negligible cost savings between the two designs, primarily because the larger 4x4 mooring system requires larger chain diameters, which increases cost. These results provide an interesting glimpse into modeling, designing, and calculating the cost of mooring systems for large WEC arrays.

cost↗
DOE OSTI2014

Stability of Iowa mutant and wild type Aβ-peptide aggregates

Recent experiments indicate a connection between the structure of amyloid aggregates and their cytotoxicity as related to neurodegenerative diseases. Of particular interest is the Iowa Mutant, which causes early-onset of Alzheimer's disease. While wild-type Amyloid β-peptides form only parallel beta-sheet aggregates, the mutant also forms meta-stable antiparallel beta sheets. Since these structural variations may cause the difference in the pathological effects of the two Aβ-peptides, we have studied in silico the relative stability of the wild type and Iowa mutant in both parallel and antiparallel forms. We compare regular molecular dynamics simulations with such where the viscosity of the samples is reduced, which, we show, leads to higher sampling efficiency. By analyzing and comparing these four sets of all-atom molecular dynamics simulations, we probe the role of the various factors that could lead to the structural differences. Our analysis indicates that the parallel forms of both wild type and Iowa mutant aggregates are stable, while the antiparallel aggregates are meta-stable for the Iowa mutant and not stable for the wild type. The differences result from the direct alignment of hydrophobic interactions in the in-register parallel oligomers, making them more stable than the antiparallel aggregates. The slightly higher thermodynamic stability of the Iowa mutant fibril-like oligomers in its parallel organization over that in antiparallel form is supported by previous experimental measurements showing slow inter-conversion of antiparallel aggregates into parallel ones. Knowledge of the mechanism that selects between parallel and antiparallel conformations and determines their relative stability may open new avenues for the development of therapies targeting familial forms of early-onset Alzheimer's disease.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2014

Molecular dynamics analysis of metal surface sputtering due to bombardment of high energy particles

Dependence of sputtering yield of Cu (100) and Ni (100) metal surface by bombardment of 200 Ar ions at various energies and angles of projections is investigated in this paper. The sputtering yield has been calculated by performing molecular dynamics simulation and the same is compared with experiments and theoretical predictions wherever possible. Additionally the kinetic energy, velocity and scattering angle distribution for sputtered and incident atoms are also observed. The results obtained from the present molecular dynamics simulations are found to be in good agreement with experimental data and theoretical estimates. It is observed that the sputtering yield increases as the energy of the bombarding ion increases. Furthermore as the incidence angle increases, the sputtering yield increases until a specific angle and then decreases as normal incidence is approached.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2024

Release dynamics of nanodiamonds created by laser-driven shock-compression of polyethylene terephthalate

Laser-driven dynamic compression experiments of plastic materials have found surprisingly fast formation of nanodiamonds (ND) via X-ray probing. This mechanism is relevant for planetary models, but could also open efficient synthesis routes for tailored NDs. We investigate the release mechanics of compressed NDs by molecular dynamics simulation of the isotropic expansion of finite size diamond from different P-T states. Analysing the structural integrity along different release paths via molecular dynamic simulations, we found substantial disintegration rates upon shock release, increasing with the on-Hugnoiot shock temperature. We also find that recrystallization can occur after the expansion and hence during the release, depending on subsequent cooling mechanisms. Our study suggests higher ND recovery rates from off-Hugoniot states, e.g., via double-shocks, due to faster cooling. Laser-driven shock compression experiments of polyethylene terephthalate (PET) samples with in situ X-ray probing at the simulated conditions found diamond signal that persists up to 11 ns after breakout. In the diffraction pattern, we observed peak shifts, which we attribute to thermal expansion of the NDs and thus a total release of pressure, which indicates the stability of the released NDs.

36 MATERIALS SCIENCE↗
DOE OSTI2018

Identifying structural changes with unsupervised machine learning methods

In this work, unsupervised machine learning methods are used to identify structural changes using the melting point transition in classical molecular dynamics simulations as an example application of the approach. Dimensionality reduction and clustering methods are applied to instantaneous radial distributions of atomic configurations from classical molecular dynamics simulations of metallic systems over a large temperature range. Principal component analysis is used to dramatically reduce the dimensionality of the feature space across the samples using an orthogonal linear transformation that preserves the statistical variance of the data under the condition that the new feature space is linearly independent. From there, k-means clustering is used to partition the samples into solid and liquid phases through a criterion motivated by the geometry of the reduced feature space of the samples, allowing for an estimation of the melting point transition. This pattern criterion is conceptually similar to how humans interpret the data but with far greater throughput, as the shapes of the radial distributions are different for each phase and easily distinguishable by humans. The transition temperature estimates derived from this machine learning approach produce comparable results to other methods on similarly small system sizes. These results show that machine learning approaches can be applied to structural changes in physical systems.

42 ENGINEERING↗
DOE OSTI2011

Biochemical, Structural and Molecular Dynamics Analyses of the Potential Virulence Factor RipA from Yersinia pestis

Human diseases are attributed in part to the ability of pathogens to evade the eukaryotic immune systems. A subset of these pathogens has developed mechanisms to survive in human macrophages. Yersinia pestis, the causative agent of the bubonic plague, is a predominately extracellular pathogen with the ability to survive and replicate intracellularly. A previous study has shown that a novel rip (required for intracellular proliferation) operon (ripA, ripB and ripC) is essential for replication and survival of Y. pestis in postactivated macrophages, by playing a role in lowering macrophage-produced nitric oxide (NO) levels. A bioinformatics analysis indicates that the rip operon is conserved among a distally related subset of macrophage-residing pathogens, including Burkholderia and Salmonella species, and suggests that this previously uncharacterized pathway is also required for intracellular survival of these pathogens. The focus of this study is ripA, which encodes for a protein highly homologous to 4-hydroxybutyrate-CoA transferase; however, biochemical analysis suggests that RipA functions as a butyryl-CoA transferase. The 1.9 Å X-ray crystal structure reveals that RipA belongs to the class of Family I CoA transferases and exhibits a unique tetrameric state. Molecular dynamics simulations are consistent with RipA tetramer formation and suggest a possible gating mechanism for CoA binding mediated by Val227. Together, our structural characterization and molecular dynamic simulations offer insights into acyl-CoA specificity within the active site binding pocket, and support biochemical results that RipA is a butyryl-CoA transferase. We hypothesize that the end product of the rip operon is butyrate, a known anti-inflammatory, which has been shown to lower NO levels in macrophages. Thus, the results of this molecular study of Y. pestis RipA provide a structural platform for rational inhibitor design, which may lead to a greater understanding of the role of RipA in this unique virulence pathway.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2012

An approach for estimating the uncertainty in ParaDiS predictions

This report outlines an approach for computing the uncertainties in the predictions of computationally expensive models. While general, we use ParaDiS , a dislocation dynamics simulator originating in Lawrence Livermore National Laboratory, as the target application. ParaDiS is a mesoscale model, and uses submodels constructed/upscaled from microscale (molecular statics and dynamics) simulations. ParaDiS outputs, in turn, are upscaled and used in continuum (macroscale) simulations, e.g., those performed by ALE3D. This report addresses how one may quantify the uncertainties introduced by upscaling (both from microscale to mesoscale, and mesoscale to continuum), and the dependence of uncertainties in ParaDiS predictions on those of the inputs. This dependence is established via sensitivity analysis, and we address how this may be performed with a minimum of ParaDiS runs, given its immense computational cost. This includes constructing a smaller version of the model, sparse sampling of the parameter space, and exploiting the asymptotic nature of the time-evolution of the model outputs. The report concludes with a discussion of the computational resources required to perform this uncertainty quantification study.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2016

Understanding irradiation growth through atomistic simulations: Defect diffusion and clustering in α-zirconium and the influence of alloying elements - 2016-0093

Irradiation-induced structural changes of α-zirconium alloys and in particular the effect of iron were investigated by molecular dynamics simulations using embedded atom potentials derived from first-principles calculations. The simulations revealed that at temperatures between 500 and 600 K self-interstitial atoms (SIAs) diffuse rapidly in a cooperative movement, preferably parallel to basal planes (a directions; ), forming nano-clusters with an extension in and . Vacancies diffuse more slowly than SIAs and remain isolated for a longer period of time. Nano-clusters associated with SIAs cause a pronounced overall expansion in a directions, as well as local strains. Under compressive strain in the c direction, vacancy diffusivity increases in the c direction. In contrast, the diffusivity of SIAs increases in the c direction under a tensile strain in the c direction. SIA nano-clusters are highly mobile within basal planes. Vacancy clusters grow by merging, leading to a contraction in the a direction, compensating for the expansion caused by SIA nano-clusters and possibly contributing to the plateau in growth after the initial rapid expansion. At the onset of breakaway growth, possibly due to stress buildup, the vacancy nano-clusters can condense into c loops, thereby diminishing the compensation effect. The alloying elements iron, nickel, chromium, and niobium liberated from secondary phase particles under irradiation or already in solution are attracted to vacancies and SIAs and are found inside vacancy and SIA loops. The interaction of alloying elements with defect clusters is discussed, with a particular focus on iron. Iron has been found to promote cluster formation in zirconium, and the structures of zirconium-iron clusters have been analyzed. Tin is repelled by SIA clusters and only weakly attracted by vacancies. Niobium impedes the diffusion of SIAs (and therefore may increase annihilation rates with nearby vacancies) and does not destabilize vacancy or SIA clusters. Ab initio calculations of the dimensional and elastic coefficients of the intermetallic phases occurring in secondary phase particles, such as Zr{sub 2}Fe and Zr{sub 3}Fe, are presented, allowing an assessment of local strains in a zirconium matrix. Thus, novel results from extended molecular dynamics simulations provide new insights and contribute to a deeper understanding of the complex mechanisms causing irradiation-induced dimensional changes and the breakaway growth of zirconium alloys. (authors)

36 MATERIALS SCIENCE↗
DOE OSTI2016

Structural crossover in a supercooled metallic liquid and the link to a liquid-to-liquid phase transition

Time-resolved synchrotron measurements were carried out to capture the structure evolution of an electrostatically levitated metallic-glass-forming liquid during free cooling. The experimental data shows a crossover in the liquid structure at ~1000 K, about 115 K below the melting temperature and 150 K above the crystallization temperature. The structure change is characterized by a dramatic growth in the extended-range order below the crossover temperature. Molecular dynamics simulations have identified that the growth of the extended-range order was due to an increased correlation between solute atoms. These results provide structural evidence for a liquid-to-liquid-phase-transition in the supercooled metallic liquid.

Glass transitions↗
DOE OSTI2014

Demonstration of fully coupled simplified extended station black-out accident simulation with RELAP-7

The RELAP-7 code is the next generation nuclear reactor system safety analysis code being developed at the Idaho National Laboratory (INL). The RELAP-7 code develop-ment effort started in October of 2011 and by the end of the second development year, a number of physical components with simplified two phase flow capability have been de-veloped to support the simplified boiling water reactor (BWR) extended station blackout (SBO) analyses. The demonstration case includes the major components for the primary system of a BWR, as well as the safety system components for the safety relief valve (SRV), the reactor core isolation cooling (RCIC) system, and the wet well. Three scenar-ios for the SBO simulations have been considered. Since RELAP-7 is not a severe acci-dent analysis code, the simulation stops when fuel clad temperature reaches damage point. Scenario I represents an extreme station blackout accident without any external cooling and cooling water injection. The system pressure is controlled by automatically releasing steam through SRVs. Scenario II includes the RCIC system but without SRV. The RCIC system is fully coupled with the reactor primary system and all the major components are dynamically simulated. The third scenario includes both the RCIC system and the SRV to provide a more realistic simulation. This paper will describe the major models and dis-cuss the results for the three scenarios. The RELAP-7 simulations for the three simplified SBO scenarios show the importance of dynamically simulating the SRVs, the RCIC sys-tem, and the wet well system to the reactor safety during extended SBO accidents.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗
DOE OSTI2016

Shock induced phase transition of water: Molecular dynamics investigation

Molecular dynamics simulations were carried out using numerous force potentials to investigate the shock induced phenomenon of pure bulk liquid water. Partial phase transition was observed at single shock velocity of 4.0 km/s without requirement of any external nucleators. Change in thermodynamic variables along with radial distribution function plots and spectral analysis revealed for the first time in the literature, within the context of molecular dynamic simulations, the thermodynamic pathway leading to formation of ice VII from liquid water on shock loading. The study also revealed information for the first time in the literature about the statistical time-frame after passage of shock in which ice VII formation can be observed and variations in degree of crystallinity of the sample over the entire simulation time of 100 ns.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2020

Damage initiation and evolution in Al-Si layered microstructures under shock loading conditions at atomic scales

Designing materials with microstructural features like multiphase interfaces have shown significant promise for usage in the next generation defense and nuclear applications. The dynamic response of these interfaces in extreme environments is observed to vary with the deformability of individual phases, which could subsequently alter the favored damage nucleation sites related to spall failure. Here, we investigate the role of spacing of interfaces in a nanocrystalline layered Aluminum-Silicon system on the shock wave propagation behavior, and microstructural and defect evolution using classical molecular dynamics simulations. The simulations are carried out with different hypothetical Al/Si microstructures including variations in the distribution of Si grains as layers in a nanocrystalline Al matrix. The molecular dynamics simulations suggest that spall failure is preferentially initiated at Al/Si interfaces. In addition, for the same system volume and same concentration of Si, a higher number of layers is marked by an increase in shock wave velocity and reduced resistance to spall failure.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Structural determinants of protocadherin-15 mechanics and function in hearing and balance perception

The vertebrate inner ear, responsible for hearing and balance, is able to sense minute mechanical stimuli originating from an extraordinarily broad range of sound frequencies and intensities or from head movements. Integral to these processes is the tip-link protein complex, which conveys force to open the inner-ear transduction channels that mediate sensory perception. Protocadherin-15 and cadherin-23, two atypically large cadherins with 11 and 27 extracellular cadherin (EC) repeats, are involved in deafness and balance disorders and assemble as parallel homodimers that interact to form the tip link. Here we report the X-ray crystal structure of a protocadherin-15 + cadherin-23 heterotetrameric complex at 2.9-Å resolution, depicting a parallel homodimer of protocadherin-15 EC1-3 molecules forming an antiparallel complex with two cadherin-23 EC1-2 molecules. In addition, we report structures for 10 protocadherin-15 fragments used to build complete high-resolution models of the monomeric protocadherin-15 ectodomain. Molecular dynamics simulations and validated crystal contacts are used to propose models for the complete extracellular protocadherin-15 parallel homodimer and the tip-link bond. Steered molecular dynamics simulations of these models suggest conditions in which a structurally diverse and multimodal protocadherin-15 ectodomain can act as a stiff or soft gating spring. These results reveal the structural determinants of tip-link–mediated inner-ear sensory perception and elucidate protocadherin-15’s structural and adhesive properties relevant in disease.

59 BASIC BIOLOGICAL SCIENCES↗